OpenScience / Software



NanoCAD

Posted on February 28, 2001 by Dan Gezelter

A freeware nanotech design system in Java Find NanoCAD at: http://server.ccl.net/cca/software/SOURCES/JAVA/ncad/unpacked/ncad.html

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Posted in Nanotechnology | Leave a comment

SeqPup

Posted on February 28, 2001 by Dan Gezelter

SeqPup is a biological sequence editor and analysis program. Find SeqPup at: http://iubio.bio.indiana.edu/IUBio-Software+Data/molbio/seqpup/java/

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Posted in Bioinformatics | Leave a comment

SCORE

Posted on February 28, 2001 by Dan Gezelter

SCORE is an empirical method developed for estimating the binding affinity of protein-ligand complex with known three-dimensional structure. Find SCORE at: http://mdl.ipc.pku.edu.cn/drug_design/work/score.html

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RnaViz

Posted on February 28, 2001 by Dan Gezelter

RnaViz is a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files. The layout of a structure … Continue reading →

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Posted in Biochemistry | Leave a comment

Raster3D

Posted on February 28, 2001 by Dan Gezelter

Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. Find Raster3D at: http://www.bmsc.washington.edu/raster3d/raster3d.html

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Posted in Molecule Viewers and Editors | Leave a comment

Geanfammer

Posted on February 27, 2001 by Dan Gezelter

geanfammer contains divclus which divides proteinclusters into more correct domain level clusters Find Geanfammer at: http://www.mrc-lmb.cam.ac.uk/genomes/geanfammer.html

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GDPC

Posted on February 27, 2001 by Dan Gezelter

gdpc is a program for visualising molecular dynamic simulations Find GDPC at: http://www.frantz.fi/software/gdpc.php

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Posted in Molecular Dynamics | Leave a comment

MOLMOL

Posted on February 27, 2001 by Dan Gezelter

MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR. Find MOLMOL at: http://www.mol.biol.ethz.ch/wuthrich/software/molmol/

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Posted in Molecule Viewers and Editors | Leave a comment

Microsat

Posted on February 27, 2001 by Dan Gezelter

Microsat is a microsatellite distance program. Its calculations can take various aspects of the allele sizes into account. Find Microsat at: http://genetics.stanford.edu/hpgl/projects/microsat/

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Posted in Genetics | Leave a comment

LigBuilder

Posted on February 27, 2001 by Dan Gezelter

LigBuilder is a multiple-purposed program written for structure-based drug design procedure. Based on the three-dimensional structure of the target protein, it can automatically build ligand molecules within the binding pocket and subsequently screen them Find LigBuilder at: http://mdl.ipc.pku.edu.cn/drug_design/work/ligbuilder.html

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Posted in Biochemistry | Leave a comment